RetrogeneDB ID: retro_hvul_26

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:449574814..449576977(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_73746
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_55429
• Aliases: None
• Description: None

Sequence

>retro_hvul_26
ATGAAGGAGAACGCCTTCGCCGGCGAGCTCTTCGACGCGCTCGCCAGGCGCCGGGACATCTCCGGGGACAGCATCAGCAA
GGCGGAGCTGCTCGAGTTCTGGGACCAGATCTCCGACACCAGCTTCGACAGCCGCCTGCAGACCTTCTTCGACATGGTGG
ACAAGGACGCCGACGGCAGGATCACAGAGGCGGAGGTCGGGGAGATCATCCGGCTCAGCGCGGCGGCCAACGACCTCAAA
AAGATCACCGAGCGGATAGAGGAGTACGCCCGGCTCATCATGGAGGAGCTCGACCCCGACAACCTCGGCTACATCGAGCT
CTACAACCTGGAGACGCTGCTGCTGCAGGCGCCGCCGACCCAGCCGTCGCGGGGCGGGACGACCAGCAGCCGTAACCTCA
GCCAGATGCTCAGCCAGCACCTCAAGCCGACGACGGAGCCCAACCCGCTCCGCCGGTGGTACCGCCGCGCCAGCTACTTC
CTGGAGGACAACTGGCGCCGCTGCTGGGTCATCATCCTGTGGTTCTCCATCTGCGCCGGTCTCTTCGCCTGGAAGTTCGT
GCAGTACCGGCGGCGCGCCGTGTTCGAGGTGATGGGCTACTGCGTGTGCGTGGCCAAGGGCGGCGCCGAGACGCTCAAGT
TCAACATGGCGCTCGTCCTCCTCCCGGTGTGCCGCAACACCATCACGTGGCTCCGCAACCGCACCGCCGCGGGGCGGGTC
GTGCCGTTCGACGACAACCTCAACTTCCACAAGGTGATCGCCGCGGGGATCACCGTCGGCGCCGGGATGCACATCATCTC
CCATTTGGCGTGCGACTTCCCGCGGCTGCTGCACGCCACCGAGGAGGAGTACGAGCCGATGAAGCCCTTCTTCGGCGACG
TCCAGCCGCCCAACTACTGGTGGTTCGTCAAGGGCACGGAGGGGTGGACGGGGCTGGTGATGCTGGCGCTCATGGCCGTC
GCCTTCACGCTCGCCACGCCGTGGTTCCGCCGCGGCAGGGTGCGCCTCCCGGGGCCGCTCAGCCGGCTCACCGGCTTCAA
CGCCTTCTGGTACACGCACCACCTCTTCATCATCGTCTACGCGCTGCTCATCGTCCACGGCCACTTCCTCTACCTCACCA
AGAAGTGGCAGAAGAAGTCGACGTGGATGTACGTGGCGGCGCCGATGGTCCTGTACGCGTGCGAGCGGCTGGCGCGGGCG
CTCCGGTCGAGCGTGCGGCCGGTGAAGATACTCAAGGTGGCCGTGTACCCCGGCAACGTGCTGTCGCTGCGCTTCTCCAA
GCCCCAGGGGTTCAGGTGCAAGAGCGGGCAGTACATCTTCGTCAACTGCGCCGCCGTGTCGCCGTTCCAGTGGCACCCGT
TCTCCATCACGTCGGCGCCGCACGACGACTACATCAGCGTCCACATCAGGACGCTCGGCGACTGGACCCGGGAGCTCAAG
AGCGTCTTCTCCAAGGTTTGCAGGCCGCCGACGGACGGGAAGAGCGGGCTGCTCCGCGCGGAGTACGCGGGCGACGGCGG
CGCCATGCCCAGCCCGAGCAGCTTCCCAACGGTGCTGATCGACGGGCCGTACGGCGCGCCGGCGCAGGACTACAAGCAGT
ACGACGTGGTGCTGCTGGTGGGGCTGGGCATCGGGGCCACGCCCATGATCTCCATCATCAAGGACATCATCAACAACATG
AAGCGGCTCGACGGCGACATCGAGTCCGGCAGCCCCAGCGACAGGAGCGTGTCGGCGGCGTCGTTCCAGACCCGGCGGGC
CTACTTCTACTGGGTGACGCGGGAGGAAGGCTCCTTCGACTGGTTCCGCGGCGTCATGGACGAGGTGGCCGAGAGCGACA
AGAAGGGCATCATCGAGCTCCACAACTACTGCACCAGCGTGTACGAGGAAGGGGACGCCCGGTCGGCGCTCATCGCCATG
CTCCAGTCCCTCAACCACGCCAAGCACGGCGTCGACGTCGTCTCCGGCACCCGCGTGAAGACGCACTTCGCCCGCCCGAA
CTGGCGCAAGGTGTACAAGGACATCGCCCTGAAGCACGCCGGGCAGCGAGTCGGAGTGTTCTACTGCGGCGCGCCGGTGC
TGATCAAGGAGCTGCGCCAGCTTGCCCAAGATTTCTCGAGGAAGACGAGCACCAAATTCGAGTTCCACAAGGAGAATTTT
TAA

Alignment

ORF - retro_hvul_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 83.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKELAFAGELFDALARRRNIAGDSISKAELLEFWDQISDTSFDSRLQTFFDMVDKDADGRITEEEVKEII
          MKE.AFAGELFDALARRR.I.GDSISKAELLEFWDQISDTSFDSRLQTFFDMVDKDADGRITE.EV.EII
Retrocopy MKENAFAGELFDALARRRDISGDSISKAELLEFWDQISDTSFDSRLQTFFDMVDKDADGRITEAEVGEII

Parental  TLSATANNLTKVKDQSEEYARLIMEELDPNNLGYIELYNLEMLLLQAP-SQSMAIGTTNSRNLSQMLSQH
          .LSA.AN.L.K.....EEYARLIMEELDP.NLGYIELYNLE.LLLQAP..Q....GTT.SRNLSQMLSQH
Retrocopy RLSAAANDLKKITERIEEYARLIMEELDPDNLGYIELYNLETLLLQAPPTQPSRGGTTSSRNLSQMLSQH

Parental  LRPTAEPNPLRRWYRRVSYFLEDNWRRCWVLLLWFCICVGLFTWKFMQYRERAVFKVMGYCVCVAKGGAE
          L.PT.EPNPLRRWYRR.SYFLEDNWRRCWV..LWF.IC.GLF.WKF.QYR.RAVF.VMGYCVCVAKGGAE
Retrocopy LKPTTEPNPLRRWYRRASYFLEDNWRRCWVIILWFSICAGLFAWKFVQYRRRAVFEVMGYCVCVAKGGAE

Parental  MLKFNMALILLPVCRNTITWFRNRTAAGRFVPFDDNINFHKVIAAGISVGAGLHIISHLTCDFPRLLRAT
          .LKFNMAL.LLPVCRNTITW.RNRTAAGR.VPFDDN.NFHKVIAAGI.VGAG.HIISHL.CDFPRLL.AT
Retrocopy TLKFNMALVLLPVCRNTITWLRNRTAAGRVVPFDDNLNFHKVIAAGITVGAGMHIISHLACDFPRLLHAT

Parental  EEEYEPMKRFFGEEQPPNYWWFVKGTEGWTGLVMLVLMAIAFTLATPWFRRGRLSLPKPLNRLTGFNAFW
          EEEYEPMK.FFG..QPPNYWWFVKGTEGWTGLVML.LMA.AFTLATPWFRRGR..LP.PL.RLTGFNAFW
Retrocopy EEEYEPMKPFFGDVQPPNYWWFVKGTEGWTGLVMLALMAVAFTLATPWFRRGRVRLPGPLSRLTGFNAFW

Parental  YSHHLFIIVYALLIVHGHFLYLTKKWQKKSTWMYLAVPMILYACERLTRALRSSVRPVKILKVAVYPGNV
          Y.HHLFIIVYALLIVHGHFLYLTKKWQKKSTWMY.A.PM.LYACERL.RALRSSVRPVKILKVAVYPGNV
Retrocopy YTHHLFIIVYALLIVHGHFLYLTKKWQKKSTWMYVAAPMVLYACERLARALRSSVRPVKILKVAVYPGNV

Parental  LSLHFSKPQGFRYKSGQYIFVNCAAVSPFQWHPFSITSAPQDDYVSVHIRTLGDWTRELKNVFSKVCRPP
          LSL.FSKPQGFR.KSGQYIFVNCAAVSPFQWHPFSITSAP.DDY.SVHIRTLGDWTRELK.VFSKVCRPP
Retrocopy LSLRFSKPQGFRCKSGQYIFVNCAAVSPFQWHPFSITSAPHDDYISVHIRTLGDWTRELKSVFSKVCRPP

Parental  TEGKSGLLRAEYDRD-GAMSNP-SFPKVLIDGPYGAPAQDYKQYDIVLLVGLGIGATPMISIIKDIINNM
          T.GKSGLLRAEY..D.GAM..P.SFP.VLIDGPYGAPAQDYKQYD.VLLVGLGIGATPMISIIKDIINNM
Retrocopy TDGKSGLLRAEYAGDGGAMPSPSSFPTVLIDGPYGAPAQDYKQYDVVLLVGLGIGATPMISIIKDIINNM

Parental  KRLEGDVESGNPGDASTS-TSFRTRRAYFYWVTREQGSFEWFRGVMDEIAESDKKGVIELHNYCTSVYED
          KRL.GD.ESG.P.D.S.S..SF.TRRAYFYWVTRE.GSF.WFRGVMDE.AESDKKG.IELHNYCTSVYE.
Retrocopy KRLDGDIESGSPSDRSVSAASFQTRRAYFYWVTREEGSFDWFRGVMDEVAESDKKGIIELHNYCTSVYEE

Parental  GDARSALIAMLQSLNHAKNGVDIVSGTRVKTHFARPNWRNVYKRIALNHREQRVGVFYCGAPVLTKELRE
          GDARSALIAMLQSLNHAK.GVD.VSGTRVKTHFARPNWR.VYK.IAL.H..QRVGVFYCGAPVL.KELR.
Retrocopy GDARSALIAMLQSLNHAKHGVDVVSGTRVKTHFARPNWRKVYKDIALKHAGQRVGVFYCGAPVLIKELRQ

Parental  LAQDFSRKTNTKFEFHKENF
          LAQDFSRKT.TKFEFHKENF
Retrocopy LAQDFSRKTSTKFEFHKENF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Hordeum vulgare was not studied using RNA-Seq expression data.

ChIP-Seq

Hordeum vulgare was not studied using ChIP-Seq data.

EST

Hordeum vulgare was not studied using EST data.

TSS

Hordeum vulgare was not studied using FANTOM5 data.

Lab

retro_hvul_26 was not experimentally validated.

Homology

Retrocopy orthology:

Hordeum vulgare does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_55429	1 retrocopy	retro_hvul_26 ,